"Anyways" can be used when changing topics.
"It's pouring rain today.. Anyways, how are you?"
"Whatever" has a few uses. You can use it if you want to stop talking about a topic (but be careful, this can sound rude!)
"Why are you so angry today? Oh, whatever! I don't want to know."
Or you can use it to mark a condition
"Whatever happens, I will always love you"
I think you might be asking because they're both markers for moving on from one topic to another. "Anyways" is very casual when you do this. It's used in friendly conversation. "Whatever" sounds like the person using the word doesn't care what the other person was saying